Assembly

Import sequence graphs in Graphical Fragment Assembly (GFA) Format versions 1.0 and 2.0
### Summary The [Assembly Cytoscape3 App](http://apps.cytoscape.org/apps/assembly) imports sequence graphs in Graphical Fragment Assembly (GFA) Format versions 1.0 and 2.0 as networks into Cytoscape, applies a visual mapping for GFA record attributes to Cytoscape node and edge attributes, and applies a force directed graph layout. ### Graphical Fragment Assembly (GFA) 1.0 Format The purpose of the Graphical Fragment Assembly (GFA) Format Specification version 1.0 is to capture sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology. The GFA 1.0 format is a tab-delimited text format for describing a set of sequences and their overlap. The first field of the line identifies the type of the line: Header lines start with `H`. Segment lines start with `S`. Link lines start with `L`. A containment line starts with `C`. A path line starts with `P`. A path traversal line starts with `T`. Terminology * **Segment** a continuous sequence or subsequence. * **Link** an overlap between two segments. Each link is from the end of one segment to the beginning of another segment. The link stores the orientation of each segment and the amount of basepairs overlapping. * **Containment** an overlap between two segments where one is contained in the other. * **Path** an ordered list of traversals over oriented segments, where each consecutive pair of oriented segments are supported by a link record. Tools that support GFA 1.0 format include [ABySS](https://github.com/bcgsc/abyss), [dsh-bio](https://github.com/heuermh/dishevelled-bio), [seqwish](https://github.com/ekg/seqwish), [SPAdes](http://cab.spbu.ru/software/spades), and [vg](https://github.com/ekg/vg). The full GFA 1.0 specification can be found at https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md. ### Importing GFA 1.0 Format To import a sequence graph in GFA 1.0 Format into Cytoscape, use **File** → **Import** → **Network from Graphical Fragment Assembly (GFA) 1.0...** and select a file. Compressed files (.bgz, .bzip2, .gz) are supported. By default sequences from GFA 1.0 segment records are loaded into Cytoscape as node attributes. To skip loading sequences, uncheck the **Load sequences** checkbox. To truncate long sequences from GFA 1.0 segment records before mapping to the node label attribute, provide a limit in base pairs (bp). The default display sequence limit is 20 bp. By default GFA 1.0 path records are loaded into Cytoscape and displayed in a path and traversal view. To skip loading paths, uncheck the **Load paths** checkbox. ### Graphical Fragment Assembly (GFA) 2.0 Format Graphical Fragment Assembly (GFA) Format Specification version 2.0 is a generalization of GFA that allows one to specify an assembly graph in either less detail, e.g. just the topology of the graph, or more detail, e.g. the multi-alignment of reads giving rise to each sequence. It is further designed to be a able to represent a string graph at any stage of assembly, from the graph of all overlaps, to a final resolved assembly of contig paths with multi-alignments. Apart from meeting these needs, the extensions also supports other assembly and variation graph types. In overview, an assembly is a graph of vertices called **segments** representing sequences that are connected by **edges** that denote local alignments between the vertex sequences. One can optionally specify a collection of external sequences, called **fragments**, from which the sequence was derived (if applicable) and how they multi-align to produce the sequence. A **gap** edge concept is also introduced so that order and orientation between disjoint contigs of an assembly can be described. Finally, one can describe and attach a name to any **path** or **subgraph** in the encoded string graph. Tools that support GFA 2.0 format include [ABySS](https://github.com/bcgsc/abyss), [dsh-bio](https://github.com/heuermh/dishevelled-bio), [gfakluge](https://github.com/edawson/gfakluge), and [Gfapy](https://github.com/ggonnella/gfapy). The full GFA 2.0 specification can be found at https://github.com/GFA-spec/GFA-spec/blob/master/GFA2.md. ### Importing GFA 2.0 Format To import a sequence graph in GFA 2.0 Format into Cytoscape, use **File** → **Import** → **Network from Graphical Fragment Assembly (GFA) 2.0...** and select a file. Compressed files (.bgz, .bzip2, .gz) are supported. ### Feedback, Issues, and Feature Requests **Assembly Cytoscape3 App** is developed on GitHub at https://github.com/heuermh/dishevelled. To provide feedback, report issues, or request new features, please [create a new issue](https://github.com/heuermh/dishevelled/issues/new) or [create a new pull request](https://github.com/heuermh/dishevelled/pulls) on Github. Github provides a nice [overview on how to create a pull request](https://help.github.com/articles/creating-a-pull-request). Thank you in advance, and we appreciate your contribution!

0.9.1

Works with Cytoscape 3.7

Release Notes

Fixed issues: Use traversal records in GFA 1.0 file if already present, https://github.com/heuermh/dishevelled/issues/17

0.9

Works with Cytoscape 3.7


CYTOSCAPE 3

Version 0.9.1

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Released 13 Jan 2020

Works with Cytoscape 3.7

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